Introduction

Questions:

Broad: What determines community structure in Lake Erie during the bloom season?

Specific:

  1. Which environmental variables determine the composition of cyanobacterial taxa? Are there negative or positive correlations between different blooming genera?

  2. Are heterotrophic communities driven by associations with specific cyanobacterial taxa or by environmental fluctuations (i.e. in source and level of organic carbon)

Results

Cyanobacteria Genera

Time series of cyanobacteria genus relative abundance

## Taxonomy Table:     [14 taxa by 7 taxonomic ranks]:
##          Kingdom    Phylum          Class             Order              
## Otu00005 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00007 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00037 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionIII"    
## Otu00044 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00049 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00063 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionIV"     
## Otu00147 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00177 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00193 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionIV"     
## Otu00304 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00367 "Bacteria" "Cyanobacteria" "unclassified"    "unclassified"     
## Otu00403 "Bacteria" "Cyanobacteria" "Cyanobacteria"   "SubsectionI"      
## Otu00832 "Bacteria" "Cyanobacteria" "unclassified"    "unclassified"     
## Otu00903 "Bacteria" "Cyanobacteria" "Melainabacteria" "Obscuribacterales"
##          Family         Genus           Species   
## Otu00005 "FamilyI"      "Microcystis"   "Otu00005"
## Otu00007 "FamilyI"      "Synechococcus" "Otu00007"
## Otu00037 "FamilyI"      "Pseudanabaena" "Otu00037"
## Otu00044 "FamilyI"      "Synechococcus" "Otu00044"
## Otu00049 "FamilyI"      "unclassified"  "Otu00049"
## Otu00063 "FamilyI"      "Anabaena"      "Otu00063"
## Otu00147 "FamilyI"      "Synechococcus" "Otu00147"
## Otu00177 "FamilyI"      "Synechococcus" "Otu00177"
## Otu00193 "FamilyI"      "Anabaena"      "Otu00193"
## Otu00304 "FamilyI"      "unclassified"  "Otu00304"
## Otu00367 "unclassified" "unclassified"  "Otu00367"
## Otu00403 "FamilyI"      "unclassified"  "Otu00403"
## Otu00832 "unclassified" "unclassified"  "Otu00832"
## Otu00903 "unclassified" "unclassified"  "Otu00903"

This is weird . . .

cyanos %>%
  subset_taxa(Class == "Cyanobacteria") -> cyanos

cyanos.otu <- t(otu_table(cyanos))
cyanos.melt <- psmelt(cyanos.otu)

For all correlation analyses, I removed low abundance OTUs (mean abundance < 0.0001 of total reads per sample i.e 1.5 ) which left a total of 399 heterotroph OTUs and 11 cyanobacteria OTUs.

Associations between cyanobacteria OTUs

These are spearman correlations with bonferroni correction between cyanobacterial OTUs

## 
## Attaching package: 'psych'
## 
## The following objects are masked from 'package:scales':
## 
##     alpha, rescale
## 
## The following object is masked from 'package:ggplot2':
## 
##     %+%
OTU1 OTU2 r pvalue
Microcystis Otu00005 Pseudanabaena Otu00037 0.7927082 0.0000000
Pseudanabaena Otu00037 Microcystis Otu00005 0.7927082 0.0000000
Synechococcus Otu00177 unclassified Otu00049 0.7754939 0.0000000
unclassified Otu00049 Synechococcus Otu00177 0.7754939 0.0000000
Pseudanabaena Otu00037 unclassified Otu00049 0.6800856 0.0000001
unclassified Otu00049 Pseudanabaena Otu00037 0.6800856 0.0000000
Microcystis Otu00005 unclassified Otu00049 0.6544720 0.0000004
unclassified Otu00049 Microcystis Otu00005 0.6544720 0.0000000
Synechococcus Otu00007 Synechococcus Otu00147 0.6180487 0.0000048
Synechococcus Otu00147 Synechococcus Otu00007 0.6180487 0.0000001
Anabaena Otu00063 Anabaena Otu00193 0.6092326 0.0000082
Anabaena Otu00193 Anabaena Otu00063 0.6092326 0.0000001
Synechococcus Otu00044 unclassified Otu00049 0.6071532 0.0000092
unclassified Otu00049 Synechococcus Otu00044 0.6071532 0.0000002
unclassified Otu00049 unclassified Otu00304 0.6059249 0.0000099
unclassified Otu00304 unclassified Otu00049 0.6059249 0.0000002
Pseudanabaena Otu00037 unclassified Otu00304 0.6017182 0.0000127
unclassified Otu00304 Pseudanabaena Otu00037 0.6017182 0.0000002
Pseudanabaena Otu00037 Synechococcus Otu00177 0.5765812 0.0000515
Synechococcus Otu00177 Pseudanabaena Otu00037 0.5765812 0.0000009
Anabaena Otu00193 Microcystis Otu00005 0.5328155 0.0000083
Microcystis Otu00005 Anabaena Otu00193 0.5328155 0.0004550
Synechococcus Otu00007 Synechococcus Otu00044 0.5206310 0.0007916
Synechococcus Otu00044 Synechococcus Otu00007 0.5206310 0.0000144
Microcystis Otu00005 unclassified Otu00304 0.5127862 0.0011183
unclassified Otu00304 Microcystis Otu00005 0.5127862 0.0000203
Microcystis Otu00005 Synechococcus Otu00177 0.5100565 0.0012586
Synechococcus Otu00177 Microcystis Otu00005 0.5100565 0.0000229
unclassified Otu00049 unclassified Otu00403 0.4837055 0.0037466
unclassified Otu00403 unclassified Otu00049 0.4837055 0.0000681
Synechococcus Otu00177 unclassified Otu00403 0.4786945 0.0045647
unclassified Otu00403 Synechococcus Otu00177 0.4786945 0.0000830
Anabaena Otu00193 unclassified Otu00049 0.4696079 0.0001178
unclassified Otu00049 Anabaena Otu00193 0.4696079 0.0064806
Synechococcus Otu00177 unclassified Otu00304 0.4419616 0.0177548
unclassified Otu00304 Synechococcus Otu00177 0.4419616 0.0003228
unclassified Otu00304 Anabaena Otu00193 0.3916358 0.0016453
Anabaena Otu00193 Synechococcus Otu00177 0.3893953 0.0017590
Anabaena Otu00063 Microcystis Otu00005 0.3837188 0.0020791
unclassified Otu00403 Microcystis Otu00005 0.3823983 0.0021606
Synechococcus Otu00044 Pseudanabaena Otu00037 0.3698081 0.0030938
unclassified Otu00403 Anabaena Otu00193 0.3695369 0.0031174
unclassified Otu00403 Synechococcus Otu00044 0.3646825 0.0035665
Synechococcus Otu00177 Synechococcus Otu00044 0.3598326 0.0040716
Synechococcus Otu00044 Microcystis Otu00005 0.3576298 0.0043212
Synechococcus Otu00147 Synechococcus Otu00044 0.3383701 0.0071462
unclassified Otu00304 Anabaena Otu00063 0.2995572 0.0180150
unclassified Otu00049 Synechococcus Otu00007 0.2504802 0.0495799
unclassified Otu00403 Synechococcus Otu00147 -0.2539484 0.0464063
Synechococcus Otu00147 Anabaena Otu00063 -0.3355312 0.0076766
Anabaena Otu00193 Synechococcus Otu00147 -0.4324991 0.0004471
Synechococcus Otu00147 Anabaena Otu00193 -0.4324991 0.0245915

Heterotrophic associates

Here we will examine correlations between cyanobacteria OTUs and heterotrophic OTUs in the full community

Summary statistics for the associates

Microcystis Otu00005

The number of positive associates is 71
The number of negative associates is 30
Genera represented by positive associates:

## 
##                  Armatimonas              Blastopirellula 
##                            0                            1 
##          Candidatus_Aquiluna          Candidatus_Captivus 
##                            0                            1 
## Candidatus_Methylacidiphilum       Candidatus_Planktoluna 
##                            1                            0 
##      Candidatus_Planktophila    Candidatus_Protochlamydia 
##                            0                            1 
##               Chthoniobacter        CL500-29_marine_group 
##                            1                            2 
##              Ferruginibacter               Flavobacterium 
##                            0                            1 
##                   Fluviicola                   hgcI_clade 
##                            1                            2 
##                   Hyphomonas                      Inhella 
##                            1                            1 
##                   Lacibacter                  Limnobacter 
##                            2                            1 
##                Limnohabitans                     Meganema 
##                            0                            1 
##      MWH-UniP1_aquatic_group              Novosphingobium 
##                            1                            1 
##                   OM27_clade                   Pedobacter 
##                            0                            0 
##                 Peredibacter             Phenylobacterium 
##                            1                            1 
##                    Pirellula                 Planctomyces 
##                            4                            2 
##                   PRD01a011B               Pseudarcicella 
##                            0                            0 
##              Pseudospirillum                  Rhodobacter 
##                            0                            1 
##                  Roseiflexus                   Roseomonas 
##                            2                            1 
##             Rubellimicrobium            Sediminibacterium 
##                            1                            1 
##                    Solitalea               Sphingorhabdus 
##                            0                            0 
##                 unclassified 
##                           38

Genera represented by negative associates:

## 
##                  Armatimonas              Blastopirellula 
##                            1                            0 
##          Candidatus_Aquiluna          Candidatus_Captivus 
##                            1                            0 
## Candidatus_Methylacidiphilum       Candidatus_Planktoluna 
##                            0                            1 
##      Candidatus_Planktophila    Candidatus_Protochlamydia 
##                            1                            0 
##               Chthoniobacter        CL500-29_marine_group 
##                            0                            3 
##              Ferruginibacter               Flavobacterium 
##                            1                            2 
##                   Fluviicola                   hgcI_clade 
##                            1                            1 
##                   Hyphomonas                      Inhella 
##                            0                            0 
##                   Lacibacter                  Limnobacter 
##                            0                            0 
##                Limnohabitans                     Meganema 
##                            1                            0 
##      MWH-UniP1_aquatic_group              Novosphingobium 
##                            0                            0 
##                   OM27_clade                   Pedobacter 
##                            1                            1 
##                 Peredibacter             Phenylobacterium 
##                            0                            0 
##                    Pirellula                 Planctomyces 
##                            0                            0 
##                   PRD01a011B               Pseudarcicella 
##                            1                            1 
##              Pseudospirillum                  Rhodobacter 
##                            1                            0 
##                  Roseiflexus                   Roseomonas 
##                            0                            0 
##             Rubellimicrobium            Sediminibacterium 
##                            0                            1 
##                    Solitalea               Sphingorhabdus 
##                            1                            1 
##                 unclassified 
##                            9

Synechococcus Otu00007

The number of positive associates is 21
The number of negative associates is 6

Genera represented by positive associates:

## 
##  Candidatus_Aquirestis Candidatus_Defluviella  CL500-29_marine_group 
##                      0                      1                      1 
##                CL500-3        Flavisolibacter         Flavobacterium 
##                      2                      1                      0 
##             Nitrospira               Opitutus             Terrimonas 
##                      0                      1                      1 
##           unclassified 
##                     14

Genera represented by negative associates:

## 
##  Candidatus_Aquirestis Candidatus_Defluviella  CL500-29_marine_group 
##                      1                      0                      0 
##                CL500-3        Flavisolibacter         Flavobacterium 
##                      0                      0                      1 
##             Nitrospira               Opitutus             Terrimonas 
##                      1                      0                      0 
##           unclassified 
##                      3

Pseudanabaena Otu00037

The number of positive associates is 96
The number of negative associates is 37

Genera represented by positive associates:

## 
##                   Acidocella                   Arenimonas 
##                            1                            0 
##                  Armatimonas                 Bdellovibrio 
##                            0                            1 
##              Blastopirellula Candidatus_Methylacidiphilum 
##                            1                            2 
##      Candidatus_Planktophila    Candidatus_Protochlamydia 
##                            0                            1 
##        CL500-29_marine_group                      CL500-3 
##                            3                            1 
##               Flavobacterium                   Fluviicola 
##                            4                            2 
##                 Gemmatimonas       GKS98_freshwater_group 
##                            3                            0 
##                   hgcI_clade                   Hyphomonas 
##                            2                            1 
##                      Inhella                   Lacibacter 
##                            1                            2 
##        LD28_freshwater_group                  Limnobacter 
##                            0                            1 
##                Limnohabitans                     Meganema 
##                            0                            1 
##              Novosphingobium                   OM27_clade 
##                            1                            0 
##                     Opitutus                 Peredibacter 
##                            0                            1 
##             Phenylobacterium                    Pirellula 
##                            1                            3 
##                 Planctomyces             Polynucleobacter 
##                            2                            0 
##               Pseudarcicella              Pseudospirillum 
##                            0                            0 
##                  Rhodobacter                  Roseiflexus 
##                            1                            2 
##                   Roseomonas            Sediminibacterium 
##                            1                            1 
##                  Silanimonas                       SM1A02 
##                            1                            1 
##                    Solitalea               Sphingorhabdus 
##                            0                            0 
##                   Terrimonas                 unclassified 
##                            1                           53

Genera represented by negative associates:

## 
##                   Acidocella                   Arenimonas 
##                            0                            1 
##                  Armatimonas                 Bdellovibrio 
##                            1                            0 
##              Blastopirellula Candidatus_Methylacidiphilum 
##                            0                            0 
##      Candidatus_Planktophila    Candidatus_Protochlamydia 
##                            1                            0 
##        CL500-29_marine_group                      CL500-3 
##                            4                            0 
##               Flavobacterium                   Fluviicola 
##                            3                            0 
##                 Gemmatimonas       GKS98_freshwater_group 
##                            0                            1 
##                   hgcI_clade                   Hyphomonas 
##                            2                            0 
##                      Inhella                   Lacibacter 
##                            0                            0 
##        LD28_freshwater_group                  Limnobacter 
##                            1                            0 
##                Limnohabitans                     Meganema 
##                            1                            0 
##              Novosphingobium                   OM27_clade 
##                            0                            2 
##                     Opitutus                 Peredibacter 
##                            1                            0 
##             Phenylobacterium                    Pirellula 
##                            0                            0 
##                 Planctomyces             Polynucleobacter 
##                            0                            1 
##               Pseudarcicella              Pseudospirillum 
##                            1                            2 
##                  Rhodobacter                  Roseiflexus 
##                            0                            0 
##                   Roseomonas            Sediminibacterium 
##                            0                            1 
##                  Silanimonas                       SM1A02 
##                            0                            0 
##                    Solitalea               Sphingorhabdus 
##                            1                            1 
##                   Terrimonas                 unclassified 
##                            0                           12

Synechococcus Otu00044

The number of positive associates is 16
The number of negative associates is 3

Genera represented by positive associates:

## 
##       Candidatus_Defluviella Candidatus_Methylacidiphilum 
##                            1                            1 
##        CL500-29_marine_group                      CL500-3 
##                            0                            2 
##               Flavobacterium                  Owenweeksia 
##                            1                            0 
##             Phenylobacterium               Roseospirillum 
##                            1                            1 
##                   Terrimonas                 unclassified 
##                            1                            8

Genera represented by negative associates:

## 
##       Candidatus_Defluviella Candidatus_Methylacidiphilum 
##                            0                            0 
##        CL500-29_marine_group                      CL500-3 
##                            1                            0 
##               Flavobacterium                  Owenweeksia 
##                            0                            1 
##             Phenylobacterium               Roseospirillum 
##                            0                            0 
##                   Terrimonas                 unclassified 
##                            0                            1

unclassified Otu00049

The number of positive associates is 71
The number of negative associates is 27

Genera represented by positive associates:

## 
##              Blastopirellula Candidatus_Methylacidiphilum 
##                            1                            1 
##      Candidatus_Planktophila        CL500-29_marine_group 
##                            0                            2 
##               Flavobacterium                   Fluviicola 
##                            1                            1 
##       GKS98_freshwater_group                   hgcI_clade 
##                            0                            2 
##                      Inhella                   Lacibacter 
##                            1                            1 
##                Limnohabitans                     Meganema 
##                            0                            1 
##      MWH-UniP1_aquatic_group              Novosphingobium 
##                            1                            1 
##                   OM27_clade                   Pedobacter 
##                            0                            0 
##                 Peredibacter             Phenylobacterium 
##                            1                            1 
##                    Pirellula                 Planctomyces 
##                            4                            3 
##             Polynucleobacter               Porphyrobacter 
##                            0                            1 
##               Pseudarcicella              Pseudospirillum 
##                            0                            0 
##                  Rhodobacter                  Roseiflexus 
##                            1                            2 
##                   Roseomonas               Roseospirillum 
##                            1                            1 
##             Rubellimicrobium            Sediminibacterium 
##                            1                            1 
##                       SM1A02                    Solitalea 
##                            1                            0 
##                  Sphingobium               Sphingorhabdus 
##                            1                            0 
##                 unclassified 
##                           39

Genera represented by negative associates:

## 
##              Blastopirellula Candidatus_Methylacidiphilum 
##                            0                            0 
##      Candidatus_Planktophila        CL500-29_marine_group 
##                            1                            2 
##               Flavobacterium                   Fluviicola 
##                            2                            2 
##       GKS98_freshwater_group                   hgcI_clade 
##                            1                            3 
##                      Inhella                   Lacibacter 
##                            0                            0 
##                Limnohabitans                     Meganema 
##                            1                            0 
##      MWH-UniP1_aquatic_group              Novosphingobium 
##                            0                            0 
##                   OM27_clade                   Pedobacter 
##                            1                            1 
##                 Peredibacter             Phenylobacterium 
##                            0                            0 
##                    Pirellula                 Planctomyces 
##                            0                            0 
##             Polynucleobacter               Porphyrobacter 
##                            1                            0 
##               Pseudarcicella              Pseudospirillum 
##                            1                            1 
##                  Rhodobacter                  Roseiflexus 
##                            0                            0 
##                   Roseomonas               Roseospirillum 
##                            0                            0 
##             Rubellimicrobium            Sediminibacterium 
##                            0                            1 
##                       SM1A02                    Solitalea 
##                            0                            1 
##                  Sphingobium               Sphingorhabdus 
##                            0                            1 
##                 unclassified 
##                            7

Anabaena Otu00063

The number of positive associates is 6
The number of negative associates is 1

Genera represented by positive associates:

## 
##           Armatimonas         Blastocatella Candidatus_Aquirestis 
##                     1                     1                     1 
##              Hirschia          Planctomyces          unclassified 
##                     1                     1                     1

Genera represented by negative associates:

## 
##           Armatimonas         Blastocatella Candidatus_Aquirestis 
##                     0                     0                     0 
##              Hirschia          Planctomyces          unclassified 
##                     0                     0                     1

Synechococcus Otu00147

The number of positive associates is 40
The number of negative associates is 30
Genera represented by positive associates:

## 
##                    Aeromonas             Anaeromyxobacter 
##                            1                            2 
##                  BD1-7_clade                Brevundimonas 
##                            0                            0 
##        Candidatus_Aquirestis Candidatus_Methylacidiphilum 
##                            0                            1 
##        CL500-29_marine_group                      CL500-3 
##                            3                            2 
##              Flavisolibacter               Flavobacterium 
##                            1                            1 
##                   Fluviicola                   hgcI_clade 
##                            1                            1 
##                     Hirschia                Methylotenera 
##                            0                            0 
##                   OM27_clade                     Opitutus 
##                            0                            1 
##                   Pedobacter                 Planctomyces 
##                            1                            0 
##                  Roseiflexus             Rubellimicrobium 
##                            1                            0 
##                 Sulfuritalea                   Terrimonas 
##                            0                            1 
##                 unclassified 
##                           23

Genera represented by negative associates:

## 
##                    Aeromonas             Anaeromyxobacter 
##                            0                            0 
##                  BD1-7_clade                Brevundimonas 
##                            1                            1 
##        Candidatus_Aquirestis Candidatus_Methylacidiphilum 
##                            1                            0 
##        CL500-29_marine_group                      CL500-3 
##                            0                            0 
##              Flavisolibacter               Flavobacterium 
##                            0                            1 
##                   Fluviicola                   hgcI_clade 
##                            0                            0 
##                     Hirschia                Methylotenera 
##                            1                            1 
##                   OM27_clade                     Opitutus 
##                            1                            1 
##                   Pedobacter                 Planctomyces 
##                            0                            3 
##                  Roseiflexus             Rubellimicrobium 
##                            0                            1 
##                 Sulfuritalea                   Terrimonas 
##                            1                            0 
##                 unclassified 
##                           17

Synechococcus Otu00177

The number of positive associates is 78
The number of negative associates is 28

Genera represented by positive associates:

## 
##                   Acidocella             Anaeromyxobacter 
##                            1                            0 
##                  Armatimonas                Blastocatella 
##                            0                            1 
##              Blastopirellula                Brevundimonas 
##                            1                            1 
## Candidatus_Methylacidiphilum      Candidatus_Planktophila 
##                            1                            0 
##               Chthoniobacter        CL500-29_marine_group 
##                            1                            1 
##               Flavobacterium                   Fluviicola 
##                            1                            0 
##                 Gemmatimonas       GKS98_freshwater_group 
##                            1                            0 
##                   hgcI_clade                     Hirschia 
##                            2                            1 
##                   Hyphomonas                      Inhella 
##                            1                            1 
##        LD28_freshwater_group                     Meganema 
##                            0                            1 
##      MWH-UniP1_aquatic_group                   Pedobacter 
##                            1                            0 
##             Phenylobacterium                    Pirellula 
##                            1                            4 
##                 Planctomyces               Porphyrobacter 
##                            3                            1 
##              Prosthecobacter               Pseudarcicella 
##                            1                            0 
##                  Rhodobacter                  Roseiflexus 
##                            1                            2 
##                   Roseomonas             Rubellimicrobium 
##                            1                            1 
##            Sediminibacterium                    Solitalea 
##                            1                            0 
##                  Sphingobium               Sphingorhabdus 
##                            1                            0 
##                 unclassified 
##                           45

Genera represented by negative associates:

## 
##                   Acidocella             Anaeromyxobacter 
##                            0                            2 
##                  Armatimonas                Blastocatella 
##                            1                            0 
##              Blastopirellula                Brevundimonas 
##                            0                            0 
## Candidatus_Methylacidiphilum      Candidatus_Planktophila 
##                            0                            1 
##               Chthoniobacter        CL500-29_marine_group 
##                            0                            1 
##               Flavobacterium                   Fluviicola 
##                            1                            3 
##                 Gemmatimonas       GKS98_freshwater_group 
##                            0                            1 
##                   hgcI_clade                     Hirschia 
##                            2                            0 
##                   Hyphomonas                      Inhella 
##                            0                            0 
##        LD28_freshwater_group                     Meganema 
##                            1                            0 
##      MWH-UniP1_aquatic_group                   Pedobacter 
##                            0                            1 
##             Phenylobacterium                    Pirellula 
##                            0                            0 
##                 Planctomyces               Porphyrobacter 
##                            0                            0 
##              Prosthecobacter               Pseudarcicella 
##                            0                            1 
##                  Rhodobacter                  Roseiflexus 
##                            0                            0 
##                   Roseomonas             Rubellimicrobium 
##                            0                            0 
##            Sediminibacterium                    Solitalea 
##                            1                            1 
##                  Sphingobium               Sphingorhabdus 
##                            0                            1 
##                 unclassified 
##                           10

Anabaena Otu00193

The number of positive associates is 19
The number of negative associates is 3

Genera represented by positive associates:

## 
##             Armatimonas           Blastocatella   Candidatus_Aquirestis 
##                       1                       1                       1 
##     Candidatus_Captivus          Flavobacterium                Hirschia 
##                       1                       0                       1 
##             Limnobacter MWH-UniP1_aquatic_group               Pirellula 
##                       1                       1                       2 
##            Planctomyces             Roseiflexus        Rubellimicrobium 
##                       1                       0                       1 
##            unclassified 
##                       8

Genera represented by negative associates:

## 
##             Armatimonas           Blastocatella   Candidatus_Aquirestis 
##                       0                       0                       0 
##     Candidatus_Captivus          Flavobacterium                Hirschia 
##                       0                       1                       0 
##             Limnobacter MWH-UniP1_aquatic_group               Pirellula 
##                       0                       0                       0 
##            Planctomyces             Roseiflexus        Rubellimicrobium 
##                       0                       1                       0 
##            unclassified 
##                       1

unclassified Otu00304

The number of positive associates is 81
The number of negative associates is 31

Genera represented by positive associates:

## 
##              Acidocella            Algoriphagus             Armatimonas 
##                       1                       1                       0 
##           Blastocatella         Blastopirellula Candidatus_Planktophila 
##                       1                       1                       0 
##          Chthoniobacter   CL500-29_marine_group          Flavobacterium 
##                       1                       2                       1 
##              Fluviicola            Gemmatimonas       Haliscomenobacter 
##                       1                       1                       1 
##              hgcI_clade              Hyphomonas              Lacibacter 
##                       2                       1                       2 
##             Limnobacter           Limnohabitans                Meganema 
##                       1                       0                       1 
##           Methylorosula                 MWH-Ta3         Novosphingobium 
##                       0                       0                       1 
##              OM27_clade             Owenweeksia            Peredibacter 
##                       0                       0                       1 
##               Pirellula            Planctomyces        Polynucleobacter 
##                       2                       3                       0 
##          Pseudarcicella             Rhodobacter             Roseiflexus 
##                       0                       1                       2 
##              Roseomonas        Rubellimicrobium       Sediminibacterium 
##                       1                       1                       1 
##               Solitalea          Sphingorhabdus            unclassified 
##                       0                       0                      50

Genera represented by negative associates:

## 
##              Acidocella            Algoriphagus             Armatimonas 
##                       0                       0                       1 
##           Blastocatella         Blastopirellula Candidatus_Planktophila 
##                       0                       0                       1 
##          Chthoniobacter   CL500-29_marine_group          Flavobacterium 
##                       0                       2                       2 
##              Fluviicola            Gemmatimonas       Haliscomenobacter 
##                       3                       0                       0 
##              hgcI_clade              Hyphomonas              Lacibacter 
##                       2                       0                       0 
##             Limnobacter           Limnohabitans                Meganema 
##                       0                       1                       0 
##           Methylorosula                 MWH-Ta3         Novosphingobium 
##                       1                       1                       0 
##              OM27_clade             Owenweeksia            Peredibacter 
##                       1                       1                       0 
##               Pirellula            Planctomyces        Polynucleobacter 
##                       0                       0                       1 
##          Pseudarcicella             Rhodobacter             Roseiflexus 
##                       1                       0                       2 
##              Roseomonas        Rubellimicrobium       Sediminibacterium 
##                       0                       0                       1 
##               Solitalea          Sphingorhabdus            unclassified 
##                       1                       1                       8

unclassified Otu00403

The number of positive associates is 2
The number of negative associates is 2

Genera represented by positive associates:

## 
##       Fluviicola Rubellimicrobium     unclassified 
##                0                1                1

Genera represented by negative associates:

## 
##       Fluviicola Rubellimicrobium     unclassified 
##                1                0                1

Colonial Associates

Here we will examine differences between heterotrophic associates in the colonial fractions for microcystis and synechococcus to see which heterotrophs are assoiated because they’re actually attaching to colonies

Microcystis colonies

cyanos %>% 
  subset_taxa(Species == "Otu00005") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 6
The number of negative associates is 5

Genera represented by positive associates:

## 
##   Flavobacterium       hgcI_clade    Limnohabitans Phenylobacterium 
##                0                0                0                1 
## Polynucleobacter      Rhodobacter     unclassified 
##                0                1                4

Genera represented by negative associates:

## 
##   Flavobacterium       hgcI_clade    Limnohabitans Phenylobacterium 
##                1                1                1                0 
## Polynucleobacter      Rhodobacter     unclassified 
##                1                0                1

Synechococcus colonies Otu00007

cyanos %>% 
  subset_taxa(Species == "Otu00007") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 3
The number of negative associates is 0

Genera represented by positive associates:

## 
## CL500-29_marine_group            hgcI_clade            Terrimonas 
##                     1                     1                     1

Genera represented by negative associates:

## 
## CL500-29_marine_group            hgcI_clade            Terrimonas 
##                     0                     0                     0

Synechococcus colonies Otu00044

cyanos %>% 
  subset_taxa(Species == "Otu00044") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 0
The number of negative associates is 0

Genera represented by positive associates:

## < table of extent 0 >

Genera represented by negative associates:

## < table of extent 0 >

53um colonial associates

Microcystis colonies

cyanos %>% 
  subset_taxa(Species == "Otu00005") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 24
The number of negative associates is 4

Genera represented by positive associates:

## 
##        Blastopirellula Candidatus_Planktoluna         Flavobacterium 
##                      1                      0                      0 
##             hgcI_clade               Meganema       Phenylobacterium 
##                      1                      1                      1 
##              Pirellula            Rhodobacter             Roseomonas 
##                      1                      1                      1 
##           unclassified            Veillonella 
##                     17                      0

Genera represented by negative associates:

## 
##        Blastopirellula Candidatus_Planktoluna         Flavobacterium 
##                      0                      1                      1 
##             hgcI_clade               Meganema       Phenylobacterium 
##                      0                      0                      0 
##              Pirellula            Rhodobacter             Roseomonas 
##                      0                      0                      0 
##           unclassified            Veillonella 
##                      1                      1

Synechococcus colonies Otu00007

cyanos %>% 
  subset_taxa(Species == "Otu00007") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 1
The number of negative associates is 0

Genera represented by positive associates:

## 
## unclassified 
##            1

Genera represented by negative associates:

## 
## unclassified 
##            0

Synechococcus colonies Otu00044

cyanos %>% 
  subset_taxa(Species == "Otu00044") %>%
  psmelt() %>%
  order_dates() -> cyanos.melt

ggplot(cyanos.melt, aes(x = Date, y = Abundance, group = Station, color = Station)) +
  geom_point() + 
  geom_line() + 
  stackbar_theme

The number of positive associates is 2
The number of negative associates is 0

Genera represented by positive associates:

## 
##     Roseomonas Roseospirillum 
##              1              1

Genera represented by negative associates:

## 
##     Roseomonas Roseospirillum 
##              0              0

Bioenv

b <- bioenv(bray.sub, env, method = "spearman", trace = T, upto = 12)
## 4095 possible subsets (this may take time...)
## No. of variables 1, No. of sets 12... done (0.3%)
## No. of variables 2, No. of sets 66... done (1.9%)
## No. of variables 3, No. of sets 220... done (7.3%)
## No. of variables 4, No. of sets 495... done (19.4%)
## No. of variables 5, No. of sets 792... done (38.7%)
## No. of variables 6, No. of sets 924... done (61.3%)
## No. of variables 7, No. of sets 792... done (80.6%)
## No. of variables 8, No. of sets 495... done (92.7%)
## No. of variables 9, No. of sets 220... done (98.1%)
## No. of variables 10, No. of sets 66... done (99.7%)
## No. of variables 11, No. of sets 12... done (100%)
## No. of variables 12, No. of sets 1... done (100%)
summary(b)
##                                                                              size
## Turbidity                                                                       1
## Temp Turbidity                                                                  2
## pH Temp Turbidity                                                               3
## pH Temp Turbidity Chla                                                          4
## pH Secchi Temp Turbidity Nitrate                                                5
## pH Temp Turbidity SRP Nitrate ParMC                                             6
## pH Secchi Temp Turbidity SRP Nitrate ParMC                                      7
## pH Secchi Temp Turbidity SRP Nitrate Chla ParMC                                 8
## pH Secchi Temp Turbidity SRP Nitrate Chla ParMC Phycocyanin                     9
## pH Secchi Temp Turbidity SRP Nitrate Ammonia Chla ParMC Phycocyanin            10
## pH Secchi Temp Turbidity SRP POC Nitrate Ammonia Chla ParMC Phycocyanin        11
## pH Secchi Temp Turbidity SRP POC Nitrate Ammonia H2O2 Chla ParMC Phycocyanin   12
##                                                                              correlation
## Turbidity                                                                         0.4355
## Temp Turbidity                                                                    0.4798
## pH Temp Turbidity                                                                 0.5048
## pH Temp Turbidity Chla                                                            0.5002
## pH Secchi Temp Turbidity Nitrate                                                  0.4909
## pH Temp Turbidity SRP Nitrate ParMC                                               0.4840
## pH Secchi Temp Turbidity SRP Nitrate ParMC                                        0.4759
## pH Secchi Temp Turbidity SRP Nitrate Chla ParMC                                   0.4642
## pH Secchi Temp Turbidity SRP Nitrate Chla ParMC Phycocyanin                       0.4461
## pH Secchi Temp Turbidity SRP Nitrate Ammonia Chla ParMC Phycocyanin               0.4245
## pH Secchi Temp Turbidity SRP POC Nitrate Ammonia Chla ParMC Phycocyanin           0.3790
## pH Secchi Temp Turbidity SRP POC Nitrate Ammonia H2O2 Chla ParMC Phycocyanin      0.3104
# Select best variables from env
env %>%
  select(pH, Temp, Turbidity) -> env.subset

# Scale env variables and calculate euclidean distance
env.scale <- scale(env.subset)
env.dist <- dist(env.scale, method = "euclidean")

# Run partial mantel 
mantel(bray.sub, env.dist, method = "spearman")
## 
## Mantel statistic based on Spearman's rank correlation rho 
## 
## Call:
## mantel(xdis = bray.sub, ydis = env.dist, method = "spearman") 
## 
## Mantel statistic r: 0.5048 
##       Significance: 0.001 
## 
## Upper quantiles of permutations (null model):
##    90%    95%  97.5%    99% 
## 0.0818 0.1100 0.1351 0.1727 
## Permutation: free
## Number of permutations: 999

Here we will construct a regression tree with phototroph abundance as reponse and environmental conditions as predictors to understand the bottom up conditions that determine community of phototrophs

. . . in progress